One thing everyone seems to miss is the fact that John does NOT have shields in the trailer. If he did, then we would see it as the wind blows the sand that SHOULD be bouncing off it.

The armor (as stated by others) is clearly battered and cracked. It's (supposingly) the same armor from Halo2 (but with upgrades). This means it's been through a LOT. don't forget he did crash land back on earth via a scrap of metal. The armor may be in dire need of repairs. The cloth seems to cling to his body more then if there was armor. Maybe he had to ditch a lot of it for his journey.

Sand is sand. If causes a LOT of damage to equipment. Regardless of how well it's sealed tight, sand WILL find a way in. Same goes for water. However, where water will eventually evaporate, sand will not. Instead, sand clumps up. It often creates a new seal/plug that spreads apart components as it does this. Taking in what we know about MC's armor, it needs to breath to allow change in internal temperature. It also doesn't have a limited supply of oxygen. When possible, the oxygen support system allows fresh oxygen in for the wearer. Now with a clearly very large dessert to walk, the flow of oxygen air and the adjustment of internal temperatures are vital to the person's survival. If sand builds up around those vents/fans, then there's BIG problem. Especially without a A.I to monitor it for you.

The clock is clearly to protect the armor's venting system. And thus to protect the Master Chief.
It's also a advertising gimmick.

As for the A.I. chip, we already know it's not Cortana's. That one was destroyed in Halo4. If you look at it again, you'll see that it's not damaged at all. Cortana's was (a number of times). This chip is clearly a replacement chip. Then whynot keep it in his helmet? Maybe because it's empty. Maybe because he doesn't want to risk another A.I. being placed in his head. Maybe because he doesn't want to clutter any of it's space with his memories in the off chance he finds her again. Or simply because he wants easy access to it as a reminder of Cortana.

Personally, I see the Chip as a dear friend's Dogtag. And thus it was attached to his own tags to keep it safe. For a Spartan 2 has a much better chance of loosing his helmet then his head. It's simply Cortana's replacement Dog Tags.